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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Distribution of Cavity similarities measured by Shaper
You can zoom onto the graph by using the mouse to make a selection

Cavities are compared using Shaper.
For more information, please see the following publication: Desaphy J. et al. Comparison and Druggability Prediction of protein-Ligand Binding sites from pharmacophore-annotated cavity shapes J. Chem. Inf. Model., 2012, 52(8), pp2287-2299

Reference Protein Data Bank Entry :
PDB ID HET Uniprot Name EC Number
2wzwNDPNitroreductase NfnB

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity		 Align
2wzwNDPNitroreductase NfnB/1.000
2zs8ADPPantothenate kinase2.7.1.330.482
3p62FMNPentaerythritol tetranitrate reductase/0.480
4loh1SYStimulator of interferon genes protein/0.480
4w5kPLPAspartate aminotransferase, mitochondrial/0.479
1h50FMNPentaerythritol tetranitrate reductase/0.474
1h51FMNPentaerythritol tetranitrate reductase/0.473
4f5dC2EStimulator of interferon genes protein/0.473
3atzFMNProstaglandin F2a synthase/0.472
1npdNADQuinate/shikimate dehydrogenase/0.470
3b4yF42F420-dependent glucose-6-phosphate dehydrogenase/0.469
1o9bNAIQuinate/shikimate dehydrogenase/0.468
3qbjNXZDipeptidyl peptidase 4/0.468
4rnuFMNNADPH dehydrogenase 11.6.99.10.468
3t4eNADQuinate/shikimate dehydrogenase/0.467
2g1n1IGRenin3.4.23.150.466
2gevCOKPantothenate kinase2.7.1.330.466
1x1aSAMC-20 methyltransferase/0.465
1x1dSAHC-20 methyltransferase/0.463
3eu5GBOProtein farnesyltransferase subunit beta2.5.1.580.463
4jyzATPGlutamine--tRNA ligase6.1.1.180.461
1z44FMNNADPH dehydrogenase/0.460
2hs6FMN12-oxophytodienoate reductase 31.3.1.420.460
3af1GDPPantothenate kinase2.7.1.330.460
3hl0NADMaleylacetate reductase/0.459
1ni1HFPProtein farnesyltransferase subunit beta2.5.1.580.458
1ni12C5Protein farnesyltransferase subunit beta2.5.1.580.458
3mj4URMUDP-galactopyranose mutase/0.458
1w34FADFerredoxin--NADP reductase1.18.1.20.456
4hmz18TdTDP-4-dehydro-6-deoxyglucose 3-epimerase5.1.3.270.456
1vi2NADQuinate/shikimate dehydrogenase/0.455
1fapRAPPeptidyl-prolyl cis-trans isomerase FKBP1A5.2.1.80.454
1fapRAPSerine/threonine-protein kinase mTOR2.7.11.10.454
1mqeAPRMutT/nudix family protein/0.454
2cv2GSUGlutamate--tRNA ligase6.1.1.170.454
2zvcSAHPrecorrin-3 C17-methyltransferase/0.454
4egbNADdTDP-glucose 4,6-dehydratase/0.454
3jyqNADQuinate/shikimate dehydrogenase (NAD(+))/0.453
4j4nD44Peptidylprolyl isomerase/0.453
4jicFMNGTN Reductase/0.453
3fapARDPeptidyl-prolyl cis-trans isomerase FKBP1A5.2.1.80.452
3fapARDSerine/threonine-protein kinase mTOR2.7.11.10.452
3sxjSAMPutative methyltransferase/0.452
5cflC2EStimulator of interferon genes protein/0.451
3h3qH13Collagen type IV alpha-3-binding protein/0.450
3intGDUUDP-galactopyranose mutase5.4.99.90.450
3rbaCODPhosphopantetheine adenylyltransferase/0.450
3f03FMNPentaerythritol tetranitrate reductase/0.449
4c13UMLUDP-N-acetylmuramoyl-L-alanyl-D-glutamate--L-lysine ligase/0.449
4drjRAPSerine/threonine-protein kinase mTOR2.7.11.10.449
4drjRAPPeptidyl-prolyl cis-trans isomerase FKBP45.2.1.80.449
2a5hSAML-lysine 2,3-aminomutase5.4.3.20.448
3e32ED2Protein farnesyltransferase subunit beta2.5.1.580.448
3i0pNADMalate dehydrogenase, putative/0.448
3jypNADQuinate/shikimate dehydrogenase (NAD(+))/0.448
3wqmB29Diterpene synthase3.1.7.80.448
4yp12BAStimulator of interferon genes protein/0.448
1gtrATPGlutamine--tRNA ligase6.1.1.180.447
1s63778Protein farnesyltransferase subunit beta2.5.1.580.447
2q1uNADPutative nucleotide sugar epimerase/ dehydratase/0.447
3atyFMNProstaglandin F2a synthase/0.447
3fr5I4AFatty acid-binding protein, adipocyte/0.447
1n2hPAJPantothenate synthetase6.3.2.10.446
2hs8FMN12-oxophytodienoate reductase 31.3.1.420.446
1icsFMN12-oxophytodienoate reductase 11.3.1.420.445
1nupNMNNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.445
1nvtNAPShikimate dehydrogenase (NADP(+))/0.445
1udaUFGUDP-glucose 4-epimerase5.1.3.20.445
2f3rG5PGuanylate kinase2.7.4.80.445
2hfuMEVMevalonate kinase/0.445
3hl4CDCCholine-phosphate cytidylyltransferase A/0.445
1ld7U66Protein farnesyltransferase subunit beta2.5.1.580.444
1q0zAKAAclacinomycin methylesterase RdmC3.1.1.950.444
1vhzAPRADP compounds hydrolase NudE3.6.10.444
3opmLUIDipeptidyl peptidase 4/0.444
1x1bSAHC-20 methyltransferase/0.443
2q1tNADPutative nucleotide sugar epimerase/ dehydratase/0.443
3enkUPGUDP-glucose 4-epimerase/0.443
3gfbNADL-threonine 3-dehydrogenase/0.443
3inrGDUUDP-galactopyranose mutase5.4.99.90.443
3lqsPSZD-alanine aminotransferase2.6.1.210.443
3tjzGNPADP-ribosylation factor 1/0.443
4bfzZVZPantothenate kinase2.7.1.330.443
4q71FADBifunctional protein PutA/0.443
1h63FMNPentaerythritol tetranitrate reductase/0.442
3s87ADPRibonucleoside-diphosphate reductase large chain 11.17.4.10.442
4br0AU1Ectonucleoside triphosphate diphosphohydrolase 2/0.442
4loi1YCStimulator of interferon genes protein/0.442
5a03NDPGlucose-fructose oxidoreductase/0.442
5kwvANPPantothenate synthetase/0.442
1kbiFMNCytochrome b2, mitochondrial1.1.2.30.441
1ld8U49Protein farnesyltransferase subunit beta2.5.1.580.441
1rkwPNTHTH-type transcriptional regulator QacR/0.441
2g226IGRenin3.4.23.150.441
2pzjNADPutative nucleotide sugar epimerase/ dehydratase/0.441
3e34ED1Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha/0.441
3e34ED1Protein farnesyltransferase subunit beta2.5.1.580.441
4bfvZVVPantothenate kinase2.7.1.330.441
4gz612VUDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit/0.441
1qrsATPGlutamine--tRNA ligase6.1.1.180.440
1sa5BMVProtein farnesyltransferase subunit beta2.5.1.580.440
2fxv5GPXanthine phosphoribosyltransferase2.4.2.220.440
3jyoNADQuinate/shikimate dehydrogenase (NAD(+))/0.440
3p74FMNPentaerythritol tetranitrate reductase/0.440
4mrm2BYGamma-aminobutyric acid type B receptor subunit 1/0.440
4rnvFMNNADPH dehydrogenase 11.6.99.10.440